5UMG | pdb_00005umg

Crystal structure of dihydropteroate synthase from Klebsiella pneumoniae subsp.

• PDB DOI: https://doi.org/10.2210/pdb5UMG/pdb

• Classification: TRANSFERASE
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2017-01-27 Released: 2017-02-15 
• Deposition Author(s): Chang, C., Zhou, M., Grimshaw, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.265 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.

Inniss, N.L., Minasov, G., Chang, C., Tan, K., Kim, Y., Maltseva, N., Stogios, P., Filippova, E., Michalska, K., Osipiuk, J., Jaroszewki, L., Godzik, A., Savchenko, A., Joachimiak, A., Anderson, W.F., Satchell, K.J.F.

(2025) Microbiol Resour Announc 14: e0020025-e0020025

• PubMed: 40391899 
• DOI: https://doi.org/10.1128/mra.00200-25
• Primary Citation Related Structures: 
  5TR3, 5TV2, 5TY0, 5U1O, 5U2G, 5U47, 5UE1, 5UME, 5UMG, 5US8, 5USW, 5USX, 5UTX, 5UU6, 5UWY, 5UX9, 5V0I, 5V36, 5VDN, 5VFB, 5VH6, 5VT3, 5WI5, 5WP0, 6AON, 6AOO, 6AWA, 6AZI, 6B4O, 6B5F, 6B8D, 6BAL, 6BK7, 6BLB, 6BQ9, 6BZ0, 6C8Q, 6CMZ, 6CN1, 6CZP, 6E5Y, 6MUQ, 6N0I, 6N7F, 6NBK, 6NFP, 6NKJ, 6PO4, 6PU9, 6PUA, ... Search all related entries


• PubMed Abstract: 
  

  Antibiotic resistance remains a leading cause of severe infections worldwide. Small changes in protein sequence can impact antibiotic efficacy. Here, we report deposition of 58 X-ray crystal structures of bacterial proteins that are known targets for antibiotics, which expands knowledge of structural variation to support future antibiotic discovery or modifications.

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Organizational Affiliation: 
• Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA.
Center for Structural Biology of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA.
Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, Illinois, USA.
Biozone, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
Biosciences Division, University of California, Riverside, School of Medicine, Riverside, California, USA.
Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.
Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 61.87 kDa 
• Atom Count: 3,889 
• Modeled Residue Count: 512 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydropteroate synthase	A, B	282	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0  Gene Names: folP, KPN_03587 EC: 2.5.1.15
UniProt
Find proteins for A6TEJ6 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6TEJ6  Go to UniProtKB:  A6TEJ6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.265 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35umg

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.313	α = 90
b = 78.313	β = 90
c = 150.324	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-15 
Deposition Author(s): Chang, C., Zhou, M., Grimshaw, S., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2017-02-15
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2026-03-25
  Changes: Database references